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Old 07-07-2011, 06:53 AM   #1
naumenko.sa
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Location: Moscow

Join Date: May 2011
Posts: 5
Default VCFtools Vcf.pm problem - broken VCF header on 1000genomes data

Hi, all!

I've tried to apply standard Vcf.pm example to SNP data file from 1000 genomes project:

use Vcf;
my $vcf = Vcf->new(file=>'ALL.2of4intersection.20100804.genotypes.vcf.gz',region=>'1:1000-2000');
$vcf->parse_header();

The file is bgzipped and tabix'ed.

And there is an error:
"Broken VCF header, no column names?"

With another small vcf file all is ok.

What is wrong?

Thank you!
SN
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Old 07-08-2011, 04:17 AM   #2
naumenko.sa
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Location: Moscow

Join Date: May 2011
Posts: 5
Default

Hi, naumenko.sa!

Vcf.pm could not open bgzipped file. So right code is
my $vcf = Vcf->new(file=>'ALL.2of4intersection.20100804.genotypes.vcf',region=>'1:1000-2000');

But plain vcf file size is 478G comparing with 63G for bgzipped one.

So dont use Perl wrapper for big files.

SN
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